Looks like my poor betta has the early stages of fin rot. Just got him from petco, where he probably didnt have the best care.. Tips of his tail fins are blackish and are fairly transparent. They don't look quite right.

I didn't want to give him a strong antibiotic treatment (Maracyn 2, etc) because his fin rot seems to be just starting (?), so I've been doing 100% water changes and dosing him with Maracyn-Oxy for each day. Has anyone had experience using it?

It says the treatment should be no longer than 5 days.. how can I tell if it has worked after 5 days? Do i try another treatment right away if this doesn't work?

I wouldn't go for an antibiotic for just a bit of fin rot, if that's even what it is. Like OFL said, some discoloration can be a sign of regrowth, particularly whitish and clear areas. However, if the fin has a black, crusty outline, it is likely infected.

Usually the infection will go away with clean water and warm, stable temperatures. You could use the salt treatment for a few days, but once I see regrowth on the fin, I stop using the salt since long term use of salt puts unnecessary strain on the fish's internal organs.

I would only use antibiotics if the infection was severe and spreading quickly, and the fish was acting lethargic and ill. Using antibiotics comes with consequences--here is a good article that you should really read before you ever use antibiotics to treat your fish: http://edis.ifas.ufl.edu/fa084 it goes over the risks and proper use of antibiotics very thoroughly.